Merged
Conversation
…to melt upon relaxation in oxDNA
dave-doty
approved these changes
Jul 29, 2021
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
in the oxDNA export function, the file format requires several vectors (r, b, and n as per https://dna.physics.ox.ac.uk/index.php/Documentation) to describe each nucleotides position and orientation in space. Nucleotides belonging to the forward strand of a helix are expected to have opposite oriented n vectors from those belonging to backward strands.
Incorrect signs don't result in significant visual differences in the generated oxDNA files when visualized; however they do cause the forces to be calculated incorrectly when the files are simulated in oxDNA causing helices to melt.
This change fixes those sign errors.